Publications

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2024

Jadhav, B., Garg, P., van Vugt, J. J. F. A., Ibanez, K., Gagliardi, D., Lee, W., Shadrina, M., Mokveld, T., Dolzhenko, E., Martin-Trujillo, A., Gies, S. J., Altman, G., Rocca, C., Barbosa, M., Jain, M., Lahiri, N., Lachlan, K., Houlden, H., Paten, B., … Sharp, A. J. (2024). A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability. Nature Genetics, 56(11), 2322–2332. https://doi.org/10.1038/s41588-024-01917-1 

Kaur, G., Perteghella, T., Carbonell-Sala, S., Gonzalez-Martinez, J., Hunt, T., Mądry, T., Jungreis, I., Arnan, C., Lagarde, J., Borsari, B., Sisu, C., Jiang, Y., Bennett, R., Berry, A., Cerdán-Vélez, D., Cochran, K., Vara, C., Davidson, C., Donaldson, S., … Guigó, R. (2024). GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing. In bioRxiv. https://doi.org/10.1101/2024.10.29.620654 

Kolesnikov, A., Cook, D., Nattestad, M., Brambrink, L., McNulty, B., Gorzynski, J., Goenka, S., Ashley, E. A., Jain, M., Miga, K. H., Paten, B., Chang, P.-C., Carroll, A., & Shafin, K. (2024). Local read haplotagging enables accurate long-read small variant calling. Nature Communications, 15(1), 5907. https://doi.org/10.1038/s41467-024-50079-5 

Logsdon, G. A., Ebert, P., Audano, P. A., Loftus, M., Porubsky, D., Ebler, J., Yilmaz, F., Hallast, P., Prodanov, T., Yoo, D., Paisie, C. A., Harvey, W. T., Zhao, X., Martino, G. V., Henglin, M., Munson, K. M., Rabbani, K., Chin, C.-S., Gu, B., … Marschall, T. (2024). Complex genetic variation in nearly complete human genomes. In bioRxiv. https://doi.org/10.1101/2024.09.24.614721 

Mastoras, M., Asri, M., Brambrink, L., Hebbar, P., Kolesnikov, A., Cook, D. E., Nattestad, M., Lucas, J., Won, T. S., Chang, P.-C., Carroll, A., Paten, B., & Shafin, K. (2024). Highly accurate assembly polishing with DeepPolisher. In bioRxiv. https://doi.org/10.1101/2024.09.17.613505 

McDaniel, J. H., Patel, V., Olson, N. D., He, H.-J., He, Z., Cole, K. D., Schmitt, A., Sikkink, K., Sedlazeck, F. J., Doddapaneni, H., Jhangiani, S. N., Muzny, D. M., Gingras, M.-C., Mehta, H., Paulin, L. F., Hastie, A. R., Yu, H.-C., Weigman, V., Rojas, A., … Zook, J. M. (2024). Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair. In bioRxiv. https://doi.org/10.1101/2024.09.18.613544 

Mudge, J. M., Carbonell-Sala, S., Diekhans, M., Martinez, J. G., Hunt, T., Jungreis, I., Loveland, J. E., Arnan, C., Barnes, I., Bennett, R., Berry, A., Bignell, A., Cerdán-Vélez, D., Cochran, K., Cortés, L. T., Davidson, C., Donaldson, S., Dursun, C., Fatima, R., … Frankish, A. (2024). GENCODE 2025: reference gene annotation for human and mouse. Nucleic Acids Research. https://doi.org/10.1093/nar/gkae1078 

Negi, S., Stenton, S. L., Berger, S. I., McNulty, B., Violich, I., Gardner, J., Hillaker, T., O’Rourke, S. M., O’Leary, M. C., Carbonell, E., Austin-Tse, C., Lemire, G., Serrano, J., Mangilog, B., VanNoy, G., Kolmogorov, M., Vilain, E., O’Donnell-Luria, A., Délot, E., … Paten, B. (2024). Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection. In medRxiv. https://doi.org/10.1101/2024.08.22.24312327 

Novak, A. M., Chung, D., Hickey, G., Djebali, S., Yokoyama, T. T., Garrison, E., Narzisi, G., Paten, B., & Monlong, J. (2024). Efficient indexing and querying of annotations in a pangenome graph. In bioRxiv. https://doi.org/10.1101/2024.10.12.618009 

Park, J., Cook, D. E., Chang, P.-C., Kolesnikov, A., Brambrink, L., Mier, J. C., Gardner, J., McNulty, B., Sacco, S., Keskus, A., Bryant, A., Ahmad, T., Shetty, J., Zhao, Y., Tran, B., Narzisi, G., Helland, A., Yoo, B., Pushel, I., … Shafin, K. (2024). DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. In bioRxiv. https://doi.org/10.1101/2024.08.16.608331 

Sirén, J., Eskandar, P., Ungaro, M. T., Hickey, G., Eizenga, J. M., Novak, A. M., Chang, X., Chang, P.-C., Kolmogorov, M., Carroll, A., Monlong, J., & Paten, B. (2024). Personalized pangenome references. Nature Methods, 21(11), 2017–2023. https://doi.org/10.1038/s41592-024-02407-2 

Yoo, D., Rhie, A., Hebbar, P., Antonacci, F., Logsdon, G. A., Solar, S. J., Antipov, D., Pickett, B. D., Safonova, Y., Montinaro, F., Luo, Y., Malukiewicz, J., Storer, J. M., Lin, J., Sequeira, A. N., Mangan, R. J., Hickey, G., Anez, G. M., Balachandran, P., … Eichler, E. E. (2024). Complete sequencing of ape genomes. In bioRxiv. https://doi.org/10.1101/2024.07.31.605654 

Gaddis, N., Fortriede, J., Guo, M., Bardes, E. E., Kouril, M., Tabar, S., Burns, K., Ardini-Poleske, M. E., Loos, S., Schnell, D., Jin, K., Iyer, B., Du, Y., Huo, B.-X., Bhattacharjee, A., Korte, J., Munshi, R., Smith, V., Herbst, A., … Salomonis, N. (2024). LungMAP portal ecosystem: Systems-level exploration of the lung. American Journal of Respiratory Cell and Molecular Biology, 70(2), 129–139. https://doi.org/10.1165/rcmb.2022-0165oc

Genner, R., Akeson, S., Meredith, M., Jerez, P. A., Malik, L., Baker, B., Miano-Burkhardt, A., Paten, B., Billingsley, K. J., Blauwendraat, C., Jain, M., & CARD-long-read Team. (2024). Assessing methylation detection for primary human tissue using Nanopore sequencing. In bioRxiv. https://doi.org/10.1101/2024.02.29.581569

Gonzalez-Ferrer, J., Lehrer, J., O’Farrell, A., Paten, B., Teodorescu, M., Haussler, D., Jonsson, V. D., & Mostajo-Radji, M. A. (2024). SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. Cell Genomics, 4(6), 100581. https://doi.org/10.1016/j.xgen.2024.100581

Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Abel, H. J., Antonacci-Fulton, L. L., Asri, M., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Buonaiuto, S., Carroll, A., Chaisson, M. J. P., Chang, P.-C., Chang, X. H., … Human Pangenome Reference Consortium. (2024). Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology, 42(4), 663–673. https://doi.org/10.1038/s41587-023-01793-w

Keskus, A., Bryant, A., Ahmad, T., Yoo, B., Aganezov, S., Goretsky, A., Donmez, A., Lansdon, L. A., Rodriguez, I., Park, J., Liu, Y., Cui, X., Gardner, J., McNulty, B., Sacco, S., Shetty, J., Zhao, Y., Tran, B., Narzisi, G., … Kolmogorov, M. (2024). Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. In bioRxiv. https://doi.org/10.1101/2024.03.22.24304756

Kuderna, L. F. K., Ulirsch, J. C., Rashid, S., Ameen, M., Sundaram, L., Hickey, G., Cox, A. J., Gao, H., Kumar, A., Aguet, F., Christmas, M. J., Clawson, H., Haeussler, M., Janiak, M. C., Kuhlwilm, M., Orkin, J. D., Bataillon, T., Manu, S., Valenzuela, A., … Farh, K. K.-H. (2024). Identification of constrained sequence elements across 239 primate genomes. Nature, 625(7996), 735–742. https://doi.org/10.1038/s41586-023-06798-8

Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H., McNulty, B., Porubsky, D., Montague, T., Lucas, J., Condon, C., Eizenga, J. M., Juul, S., McKenzie, S., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E., Axel, R., … Paten, B. (2024). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. Genome Research, 34(3). https://doi.org/10.1101/gr.278268.123

Makova, K. D., Pickett, B. D., Harris, R. S., Hartley, G. A., Cechova, M., Pal, K., Nurk, S., Yoo, D., Li, Q., Hebbar, P., McGrath, B. C., Antonacci, F., Aubel, M., Biddanda, A., Borchers, M., Bornberg-Bauer, E., Bouffard, G. G., Brooks, S. Y., Carbone, L., … Phillippy, A. M. (2024). The complete sequence and comparative analysis of ape sex chromosomes. Nature, 630(8016), 401–411. https://doi.org/10.1038/s41586-024-07473-2

Mao, Y., Harvey, W. T., Porubsky, D., Munson, K. M., Hoekzema, K., Lewis, A. P., Audano, P. A., Rozanski, A., Yang, X., Zhang, S., Yoo, D., Gordon, D. S., Fair, T., Wei, X., Logsdon, G. A., Haukness, M., Dishuck, P. C., Jeong, H., del Rosario, R., … Eichler, E. E. (2024). Structurally divergent and recurrently mutated regions of primate genomes. Cell, 187(6), 1547-1562.e13. https://doi.org/10.1016/j.cell.2024.01.052

Mirarab, S., Rivas-González, I., Feng, S., Stiller, J., Fang, Q., Mai, U., Hickey, G., Chen, G., Brajuka, N., Fedrigo, O., Formenti, G., Wolf, J. B. W., Howe, K., Antunes, A., Schierup, M. H., Paten, B., Jarvis, E. D., Zhang, G., & Braun, E. L. (2024). A region of suppressed recombination misleads neoavian phylogenomics. Proceedings of the National Academy of Sciences of the United States of America, 121(15). https://doi.org/10.1073/pnas.2319506121

Raney, B. J., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Fischer, C., Navarro Gonzalez, J., Hickey, G., Hinrichs, A. S., Kuhn, R. M., Lee, B. T., Lee, C. M., Le Mercier, P., Miga, K. H., Nassar, L. R., Nejad, P., Paten, B., … Haeussler, M. (2024). The UCSC Genome Browser database: 2024 update. Nucleic Acids Research, 52(D1), D1082–D1088. https://doi.org/10.1093/nar/gkad987

Taylor, D. J., Eizenga, J. M., Li, Q., Das, A., Jenike, K. M., Kenny, E. E., Miga, K. H., Monlong, J., McCoy, R. C., Paten, B., & Schatz, M. C. (2024). Beyond the Human Genome Project: The age of complete human genome sequences and pangenome references. Annual Review of Genomics and Human Genetics. https://doi.org/10.1146/annurev-genom-021623-081639

Wirthlin, M. E., Schmid, T. A., Elie, J. E., Zhang, X., Kowalczyk, A., Redlich, R., Shvareva, V. A., Rakuljic, A., Ji, M. B., Bhat, N. S., Kaplow, I. M., Schäffer, D. E., Lawler, A. J., Wang, A. Z., Phan, B. N., Annaldasula, S., Brown, A. R., Lu, T., Lim, B. K., … Zoonomia Consortium. (2024). Vocal learning–associated convergent evolution in mammalian proteins and regulatory elements. Science (New York, N.Y.), 383(6690). https://doi.org/10.1126/science.abn3263

2023

Ahalt, S., Avillach, P., Boyles, R., Bradford, K., Cox, S., Davis-Dusenbery, B., Grossman, R. L., Krishnamurthy, A., Manning, A., Paten, B., Philippakis, A., Borecki, I., Chen, S. H., Kaltman, J., Ladwa, S., Schwartz, C., Thomson, A., Davis, S., Leaf, A., … Asare, J. (2023). Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research. Journal of the American Medical Informatics Association: JAMIA, 30(7), 1293–1300. https://doi.org/10.1093/jamia/ocad048 

Andrews, G., Fan, K., Pratt, H. E., Phalke, N., Karlsson, E. K., Lindblad-Toh, K., Gazal, S., Moore, J. E., Weng, Z., Andrews, G., Armstrong, J. C., Bianchi, M., Birren, B. W., Bredemeyer, K. R., Breit, A. M., Christmas, M. J., Clawson, H., Damas, J., Di Palma, F., … Zoonomia Consortium§. (2023). Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn7930

Chen, S. H., Kaltman, J., Ladwa, S., Schwartz, C., Thomson, A., Davis, S., Leaf, A., … Asare, J. (2023). Building a collaborative cloud platform to accelerate heart, lung, blood, and sleep research. Journal of the American Medical Informatics Association: JAMIA, 30(7), 1293–1300. https://doi.org/10.1093/jamia/ocad048

Christmas, M. J., Kaplow, I. M., Genereux, D. P., Dong, M. X., Hughes, G. M., Li, X., Sullivan, P. F., Hindle, A. G., Andrews, G., Armstrong, J. C., Bianchi, M., Breit, A. M., Diekhans, M., Fanter, C., Foley, N. M., Goodman, D. B., Goodman, L., Keough, K. C., Kirilenko, B., … Zoonomia Consortium§. (2023). Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn3943

Fahlgren, N., Kapoor, M., Yordanova, G., Papatheodorou, I., Waese, J., Cole, B., Harrison, P., Ware, D., Tickle, T., Paten, B., Burdett, T., Elsik, C. G., Tuggle, C. K., & Provart, N. J. (2023). Toward a data infrastructure for the Plant Cell Atlas. Plant Physiology, 191(1), 35–46. https://doi.org/10.1093/plphys/kiac468

Foley, N. M., Mason, V. C., Harris, A. J., Bredemeyer, K. R., Damas, J., Lewin, H. A., Eizirik, E., Gatesy, J., Karlsson, E. K., Lindblad-Toh, K., Springer, M. S., Murphy, W. J., Andrews, G., Armstrong, J. C., Bianchi, M., Birren, B. W., Bredemeyer, K. R., Breit, A. M., Christmas, M. J., … Zoonomia Consortium‡. (2023). A genomic timescale for placental mammal evolution. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abl8189

Frankish, A., Carbonell-Sala, S., Diekhans, M., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Arnan, C., Barnes, I., Banerjee, A., Bennett, R., Berry, A., Bignell, A., Boix, C., Calvet, F., Cerdán-Vélez, D., Cunningham, F., Davidson, C., … Flicek, P. (2023). GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research, 51(D1), D942–D949. https://doi.org/10.1093/nar/gkac1071

Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Abel, H. J., Antonacci-Fulton, L. L., Asri, M., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Carroll, A., Chaisson, M. J. P., Chang, P.-C., … Human Pangenome Reference Consortium. (2023). Recombination between heterologous human acrocentric chromosomes. Nature, 617(7960), 335–343. https://doi.org/10.1038/s41586-023-05976-y

Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Abel, H. J., Antonacci-Fulton, L. L., Asri, M., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Buonaiuto, S., Carroll, A., Chaisson, M. J. P., Chang, P.-C., Chang, X. H., … Human Pangenome Reference Consortium. (2023). Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology. https://doi.org/10.1038/s41587-023-01793-w

Jadhav, B., Garg, P., van Vugt, J. J. F. A., Garikano, K. I., Gagliardi, D., Lee, W., Martin-Trujillo, A., Gies, S. L., Barbosa, M., Jain, M., Houlden, H., Paten, B., Veldink, J., Tucci, A., Sharp, A. J., Genomics England Research Consortium, & Project MinE ALS Sequencing Consortium. (2023). A GCC repeat expansion inAFF3is a significant cause of intellectual disability. In bioRxiv. https://doi.org/10.1101/2023.05.03.23289461

Jain, S., Pei, L., Spraggins, J. M., Angelo, M., Carson, J. P., Gehlenborg, N., Ginty, F., Gonçalves, J. P., Hagood, J. S., Hickey, J. W., Kelleher, N. L., Laurent, L. C., Lin, S., Lin, Y., Liu, H., Naba, A., Nakayasu, E. S., Qian, W.-J., Radtke, A., … HuBMAP Consortium. (2023). Advances and prospects for the human BioMolecular atlas program (HuBMAP). Nature Cell Biology, 25(8), 1089–1100. https://doi.org/10.1038/s41556-023-01194-w

Kaplow, I. M., Lawler, A. J., Schäffer, D. E., Srinivasan, C., Sestili, H. H., Wirthlin, M. E., Phan, B. N., Prasad, K., Brown, A. R., Zhang, X., Foley, K., Genereux, D. P., Karlsson, E. K., Lindblad-Toh, K., Meyer, W. K., Pfenning, A. R., Andrews, G., Armstrong, J. C., Bianchi, M., … Zoonomia Consortium**. (2023). Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abm7993

Keough, K. C., Whalen, S., Inoue, F., Przytycki, P. F., Fair, T., Deng, C., Steyert, M., Ryu, H., Lindblad-Toh, K., Karlsson, E., Nowakowski, T., Ahituv, N., Pollen, A., Pollard, K. S., Andrews, G., Armstrong, J. C., Bianchi, M., Birren, B. W., Bredemeyer, K. R., … Zoonomia Consortium§. (2023). Three-dimensional genome rewiring in loci with human accelerated regions. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abm1696

Kirilenko, B. M., Munegowda, C., Osipova, E., Jebb, D., Sharma, V., Blumer, M., Morales, A. E., Ahmed, A.-W., Kontopoulos, D.-G., Hilgers, L., Lindblad-Toh, K., Karlsson, E. K., Hiller, M., Andrews, G., Armstrong, J. C., Bianchi, M., Birren, B. W., Bredemeyer, K. R., Breit, A. M., … Zoonomia Consortium‡. (2023). Integrating gene annotation with orthology inference at scale. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn3107

Kolmogorov, M., Billingsley, K. J., Mastoras, M., Meredith, M., Monlong, J., Lorig-Roach, R., Asri, M., Alvarez Jerez, P., Malik, L., Dewan, R., Reed, X., Genner, R. M., Daida, K., Behera, S., Shafin, K., Pesout, T., Prabakaran, J., Carnevali, P., North American Brain Expression Consortium (NABEC), … Paten, B. (2023). Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. BioRxiv.Org: The Preprint Server for Biology. https://doi.org/10.1101/2023.01.12.523790

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., Buonaiuto, S., Chang, X. H., Cheng, H., Chu, J., Colonna, V., Eizenga, J. M., Feng, X., Fischer, C., Fulton, R. S., … Paten, B. (2023). A draft human pangenome reference. Nature, 617(7960), 312–324. https://doi.org/10.1038/s41586-023-05896-x

Lorig-Roach, R., Meredith, M., Monlong, J., Jain, M., Olsen, H., McNulty, B., Porubsky, D., Montague, T., Lucas, J., Condon, C., Eizenga, J., Juul, S., McKenzie, S., Simmonds, S. E., Park, J., Asri, M., Koren, S., Eichler, E., Axel, R., … Paten, B. (2023). Phased nanopore assembly with Shasta and modular graph phasing with GFAse. BioRxiv.Org: The Preprint Server for Biology. https://doi.org/10.1101/2023.02.21.529152

Mao, Y., Harvey, W. T., Porubsky, D., Munson, K. M., Hoekzema, K., Lewis, A. P., Audano, P. A., Rozanski, A., Yang, X., Zhang, S., Gordon, D. S., Wei, X., Logsdon, G. A., Haukness, M., Dishuck, P. C., Jeong, H., Del Rosario, R., Bauer, V. L., Fattor, W. T., … Eichler, E. E. (2023). Structurally divergent and recurrently mutated regions of primate genomes. BioRxiv.Org: The Preprint Server for Biology. https://doi.org/10.1101/2023.03.07.531415

Marco-Sola, S., Eizenga, J. M., Guarracino, A., Paten, B., Garrison, E., & Moreto, M. (2023). Optimal gap-affine alignment in O(s) space. Bioinformatics (Oxford, England), 39(2). https://doi.org/10.1093/bioinformatics/btad074

Moon, K. L., Huson, H. J., Morrill, K., Wang, M.-S., Li, X., Srikanth, K., Lindblad-Toh, K., Svenson, G. J., Karlsson, E. K., Shapiro, B., Andrews, G., Armstrong, J. C., Bianchi, M., Birren, B. W., Bredemeyer, K. R., Breit, A. M., Christmas, M. J., Clawson, H., Damas, J., … Zoonomia Consortium. (2023). ​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn5887

Osmanski, A. B., Paulat, N. S., Korstian, J., Grimshaw, J. R., Halsey, M., Sullivan, K. A. M., Moreno-Santillán, D. D., Crookshanks, C., Roberts, J., Garcia, C., Johnson, M. G., Densmore, L. D., Stevens, R. D., Rosen, J., Storer, J. M., Hubley, R., Smit, A. F. A., Dávalos, L. M., Karlsson, E. K., … Zoonomia Consortium†. (2023). Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn1430

Paulat, N. S., Storer, J. M., Moreno-Santillán, D. D., Osmanski, A. B., Sullivan, K. A. M., Grimshaw, J. R., Korstian, J., Halsey, M., Garcia, C. J., Crookshanks, C., Roberts, J., Smit, A. F. A., Hubley, R., Rosen, J., Teeling, E. C., Vernes, S. C., Myers, E., Pippel, M., Brown, T., … Zoonomia Consortium. (2023). Chiropterans are a hotspot for horizontal transfer of DNA transposons in mammalia. Molecular Biology and Evolution, 40(5). https://doi.org/10.1093/molbev/msad092

Porubsky, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., Korbel, J. O., Eichler, E. E., Human Pangenome Reference Consortium (HPRC), & Human Genome Structural Variation Consortium (HGSVC). (2023). Inversion polymorphism in a complete human genome assembly. Genome Biology, 24(1). https://doi.org/10.1186/s13059-023-02919-8

Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A. D., Stober, C., Korbel, J. O., Paten, B., Marschall, T., Eichler, E. E., & Human Pangenome Reference Consortium. (2023). Gaps and complex structurally variant loci in phased genome assemblies. Genome Research, 33(4), 496–510. https://doi.org/10.1101/gr.277334.122

Sibbesen, J. A., Eizenga, J. M., Novak, A. M., Sirén, J., Chang, X., Garrison, E., & Paten, B. (2023). Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature Methods, 20(2), 239–247. https://doi.org/10.1038/s41592-022-01731-9

Sukoff Rizzo, S. J., Homanics, G., Schaeffer, D. J., Schaeffer, L., Park, J. E., Oluoch, J., Zhang, T., Haber, A., Seyfried, N. T., Paten, B., Greenwood, A., Murai, T., Choi, S. H., Huhe, H., Kofler, J., Strick, P. L., Carter, G. W., & Silva, A. C. (2023). Bridging the rodent to human translational gap: Marmosets as model systems for the study of Alzheimer’s disease. Alzheimer’s & Dementia (New York, N. Y.), 9(3). https://doi.org/10.1002/trc2.12417

Sullivan, P. F., Meadows, J. R. S., Gazal, S., Phan, B. N., Li, X., Genereux, D. P., Dong, M. X., Bianchi, M., Andrews, G., Sakthikumar, S., Nordin, J., Roy, A., Christmas, M. J., Marinescu, V. D., Wallerman, O., Xue, J. R., Li, Y., Yao, S., Sun, Q., … Lindblad-Toh, K. (2023). Leveraging base pair mammalian constraint to understand genetic variation and human disease. BioRxiv.Org: The Preprint Server for Biology. https://doi.org/10.1101/2023.03.10.531987

Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Abel, H. J., Antonacci-Fulton, L. L., Baid, G., Baker, C. A., Belyaeva, A., Billis, K., Bourque, G., Buonaiuto, S., Carroll, A., Chaisson, M. J. P., … Human Pangenome Reference Consortium. (2023). Increased mutation and gene conversion within human segmental duplications. Nature, 617(7960), 325–334. https://doi.org/10.1038/s41586-023-05895-y

Wilder, A. P., Supple, M. A., Subramanian, A., Mudide, A., Swofford, R., Serres-Armero, A., Steiner, C., Koepfli, K.-P., Genereux, D. P., Karlsson, E. K., Lindblad-Toh, K., Marques-Bonet, T., Munoz Fuentes, V., Foley, K., Meyer, W. K., Ryder, O. A., Shapiro, B., Andrews, G., Armstrong, J. C., … Zoonomia Consortium‡. (2023). The contribution of historical processes to contemporary extinction risk in placental mammals. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn5856

Xue, J. R., Mackay-Smith, A., Mouri, K., Garcia, M. F., Dong, M. X., Akers, J. F., Noble, M., Li, X., Lindblad-Toh, K., Karlsson, E. K., Noonan, J. P., Capellini, T. D., Brennand, K. J., Tewhey, R., Sabeti, P. C., Reilly, S. K., Andrews, G., Armstrong, J. C., Bianchi, M., … Zoonomia Consortium†. (2023). The functional and evolutionary impacts of human-specific deletions in conserved elements. Science (New York, N.Y.), 380(6643). https://doi.org/10.1126/science.abn2253

2022

Aganezov S, Yan SM, Soto DC, et al. A complete reference genome improves analysis of human genetic variation. Science. 2022;376(6588):eabl3533. doi:10.1126/science.abl3533 https://doi.org/10.1126/science.abl3533

Altemose N, Logsdon GA, Bzikadze AV, et al. Complete genomic and epigenetic maps of human centromeres. Science. 2022;376(6588):eabl4178. doi:10.1126/science.abl4178 https://doi.org/10.1126/science.abl4178

Bailey AD, Talkish J, Ding H, et al. Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. Elife. 2022;11:e76562. Published 2022 Apr 6. doi:10.7554/eLife.76562 https://doi.org/10.7554/elife.76562

Gaddis, N., Fortriede, J., Guo, M., Bardes, E. E., Kouril, M., Tabar, S., Burns, K., Ardini-Poleske, M. E., Loos, S., Schnell, D., Jin, K., Iyer, B., Du, Y., Huo, B.-X., Bhattacharjee, A., Korte, J., Munshi, R., Smith, V., Herbst, A., … NHLBI LungMAP Consortium. (2022). LungMAP portal ecosystem: Systems-level exploration of the lung. American Journal of Respiratory Cell and Molecular Biology. https://doi.org/10.1165/rcmb.2022-0165oc

Goenka SD, Gorzynski JE, Shafin K, et al. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing [published online ahead of print, 2022 Mar 28]. Nat Biotechnol. 2022;10.1038/s41587-022-01221-5. doi:10.1038/s41587-022-01221-5 https://doi.org/10.1038/s41587-022-01221-5 

Gorzynski JE, Goenka SD, Shafin K, et al. Ultrarapid nanopore genome sequencing in a critical care setting. N Engl J Med. 2022;386(7):700-702. doi:10.1056/NEJMc2112090 https://doi.org/10.1056/nejmc2112090

Gorzynski JE, Goenka SD, Shafin K, et al. Ultra-rapid nanopore whole genome genetic diagnosis of dilated cardiomyopathy in an adolescent with cardiogenic shock. Circ Genom Precis Med. Published online 2022:CIRCGEN121003591. doi:10.1161/CIRCGEN.121.003591 https://doi.org/10.1161/circgen.121.003591

Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., Cheng, H., Asri, M., Logsdon, G. A., Carnevali, P., Chaisson, M. J. P., Chin, C.-S., Cody, S., Collins, J., Ebert, P., … Human Pangenome Reference Consortium. (2022). Semi-automated assembly of high-quality diploid human reference genomes. Nature, 611(7936), 519–531. https://doi.org/10.1038/s41586-022-05325-5

Markello C, Huang C, Rodriguez A, et al. A complete pedigree-based graph workflow for rare candidate variant analysis [published online ahead of print, 2022 Apr 28]. Genome Res. 2022;10.1101/gr.276387.121. doi:10.1101/gr.276387.121 https://doi.org/10.1101/gr.276387.121 

Mc Cartney AM, Shafin K, Alonge M, et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies [published online ahead of print, 2022 Mar 31]. Nat Methods. 2022;10.1038/s41592-022-01440-3. doi:10.1038/s41592-022-01440-3 https://doi.org/10.1038/s41592-022-01440-3

Nurk S, Koren S, Rhie A, et al. The complete sequence of a human genome. Science. 2022;376(6588):44-53. doi:10.1126/science.abj6987 https://doi.org/10.1126/science.abj6987 

Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Boja, E., Maier, E. J., Serang, O., Jáspez, D., Lorenzo-Salazar, J. M., Muñoz-Barrera, A., Rubio-Rodríguez, L. A., Flores, C., Kyriakidis, K., Malousi, A., Shafin, K., Pesout, T., … Zook, J. M. (2022). PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions. Cell Genomics, 2(5), 100129. https://doi.org/10.1016/j.xgen.2022.100129

Schatz MC, Philippakis AA, Afgan E, et al. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022;2(1):100085. doi:10.1016/j.xgen.2021.100085 https://doi.org/10.1016/j.xgen.2021.100085

Sirén, J., & Paten, B. (2022). GBZ file format for pangenome graphs. Bioinformatics (Oxford, England), 38(22), 5012–5018. https://doi.org/10.1093/bioinformatics/btac656

Walker, N. J., Rashid, M., Yu, S., Bignell, H., Lumby, C. K., Livi, C. M., Howell, K., Morley, D. J., Morganella, S., Barrell, D., Caim, S., Gosal, W., Füllgrabe, J., Charlesworth, T. J., Vasquez, L., Ahdesmäki, M., Eizenga, J., Prabhat, P., Proutski, V., … Holbrook, J. D. (2022). Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-20975-1

Wang T, Antonacci-Fulton L, Howe K, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 2022;604(7906):437-446. doi:10.1038/s41586-022-04601-8 https://doi.org/10.1038/s41586-022-04601-8 

2021
Cahill JA, Armstrong J, Deran A, et al. Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans. Genome Res. 2021;31(11):2035-2049. https://doi.org/10.1101/gr.275989.121

Ding H, Anastopoulos I, Bailey AD 4th, Stuart J, Paten B. Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures. Nat Commun. 2021;12(1):6545. https://doi.org/10.1038/s41467-021-26929-x

Eizenga JM, Novak AM, Kobayashi E, et al. Efficient dynamic variation graphs. Bioinformatics. 2021;36(21):5139-5144. https://doi.org/10.1093/bioinformatics/btaa640

Frankish, A., Diekhans, M., Jungreis, I., et al. GENCODE 2021. Nucleic Acids Research. 2021;49(D1):D916–D923. https://doi.org/10.1093/nar/gkaa1087

Garg P, Martin-Trujillo A, Rodriguez OL, et al. Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression. Am J Hum Genet. 2021;108(5):809-824. https://doi.org/10.1016/j.ajhg.2021.03.016

Mao Y, Catacchio CR, Hillier LW, et al. A high-quality bonobo genome refines the analysis of hominid evolution [published online ahead of print, 2021 May 5]. Nature. 2021;10.1038/s41586-021-03519-x. https://doi.org/10.1038/s41586-021-03519-x

Porubsky D, Ebert P, Audano PA, et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat Biotechnol. 2021;39(3):302-308. https://doi.org/10.1038/s41587-020-0719-5

Rhie A, McCarthy SA, Fedrigo O, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737-746. https://doi.org/10.1038/s41586-021-03451-0

Shafin K, Pesout T, Chang P-C, et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat Methods. 2021;18(11):1322-1332. https://doi.org/10.1038/s41592-021-01299-w

Sirén J, Monlong J, Chang X, et al. Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science. 2021;374(6574):abg8871. https://doi.org/10.1126/science.abg8871

Stahl-Rommel, S., Jain, M., Nguyen, H. N., et al. Real-time culture-independent microbial profiling onboard the International Space Station using nanopore sequencing. Genes. 2021;12(1):106. https://doi.org/10.3390/genes12010106

Sun, C., Huang, J., Wang, Y., et al. Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Molecular Biology and Evolution. 2021;38(2):486-501. https://doi.org/10.1093/molbev/msaa240

Yuen D, Cabansay L, Duncan A, et al. The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols [published online ahead of print, 2021 May 12]. Nucleic Acids Res. 2021;gkab346. https://doi.org/10.1093/nar/gkab346

2020

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020;587(7833), 246-251. https://doi.org/10.1038/s41586-020-2871-y

Burton, A., et al. Off Earth Identification of Bacterial Populations Using 16S rDNA Nanopore Sequencing. Genes. 2020;11:76.  https://doi.org/10.3390/genes11010076

Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Distance indexing and seed clustering in sequence graphs. Bioinformatics. 2020;36:i146-i153. https://doi.org/10.1093/bioinformatics/btaa446

Ding H, Bailey AD, Jain M, Olsen H, Paten B. Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts. Bioinformatics. 2020;601. https://doi.org/10.1093/bioinformatics/btaa601

Eizenga J, et al. Pangenome Graphs. Annual Review of Genomics and Human Genetics. 2020;21. https://doi.org/10.1146/annurev-genom-120219-080406

Eizenga, J. M., Novak, A. M., Kobayashi, E., Villani, F., Cisar, C., et al. Efficient dynamic variation graphs. Bioinformatics (Oxford, England). 2020. https://doi.org/10.1093/bioinformatics/btaa640

Eizenga J, Novak A, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E. Succinct dynamic variation graphs. bioRxiv 056317. 2020. https://doi.org/10.1101/2020.04.23.056317

ENCODE Project Consortium, Snyder MP, Gingeras TR. Perspectives on ENCODE. Nature. 2020;583(7818):693-698. https://doi.org/10.1038/s41586-020-2449-8

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., et al. Dense sampling of bird diversity increases power of comparative genomics. Nature. 2020;587(7833), 252–257. https://doi.org/10.1038/s41586-020-2873-9

Frankish, A., Diekhans, M., Jungreis, I., Lagarde, J., Loveland, J. E., et al. GENCODE 2021. Nucleic Acids Research. 2020. https://doi.org/10.1093/nar/gkaa1087

Garg P, et al. A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions. bioRxiv 007864. 2020. https://doi.org/10.1101/2020.03.25.007864

Goenka SD, Turakhia Y, Paten B, Horowitz M. SegAlign: a scalable GPU-based whole genome aligner. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE Press; 2020:1-13. https://doi.org/10.1109/SC41405.2020.00043

Goldman, M.J., et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol. 2020;38:675–678. https://doi.org/10.1038/s41587-020-0546-8

Goldman, M.J., et al. A user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020;11:3400. https://doi.org/10.1038/s41467-020-16785-6

Hickey, G., Heller, D., Monlong, J., Sibbesen, J., Siren, J., Eizenga, J., Dawson, E., Garrison, E., Novak, A., Paten, B. Genotyping structural variants in pangenome graphs using the vg toolkit. Genome Biol. 2020;21:35. https://doi.org/10.1186/s13059-020-1941-7

Katayama, T., et al. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research. 2020;9:136. https://doi.org/10.12688/f1000research.18236.1

Kessler MD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A. 2020;117(5):2560-2569. https://doi.org/10.1073/pnas.1902766117

Krasheninnikova K, Diekhans M, Armstrong J, Dievskii A, Paten B, O’Brien S. halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments. GigaScience. 2020;9:6.  https://doi.org/10.1093/gigascience/giaa047

Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology. 2020. https://doi.org/10.1038/s41587-020-0719-5

Miga, K.H., et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020. https://doi.org/10.1038/s41586-020-2547-7

Rhie A, et al. Towards complete and error-free genome assemblies of all vertebrate species. bioRxiv 110833. 2020. https://doi.org/10.1101/2020.05.22.110833 

Salama, S. R., et al. Using great ape cerebral cortex organoids to study brain evolution and disease. American Journal of Physical Anthropology. 2020;171:245.

Shafin, K., et al. Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. Nat Biotechnol. 2020. https://doi.org/10.1038/s41587-020-0503-6

Sirén J, Garrison E, Novak A, Paten B, Durbin R. Haplotype-aware graph indexes. Bioinformatics. 2020;36(2):400-407. https://doi.org/10.1093/bioinformatics/btz575

Sun C, et al. Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators. bioRxiv 122879. 2020. https://doi.org/10.1101/2020.05.29.122879

The ENCODE Project Consortium, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583:699–710. https://doi.org/10.1038/s41586-020-2493-4

Turakhia Y, De Maio N, Thornlow B, et al. Stability of SARS-CoV-2 phylogenies. PLoS Genet. 2020;16(11):e1009175. https://doi.org/10.1371/journal.pgen.1009175

Vivian J, Eizenga J, Beale H, Vaske O, Paten B. Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples. JCO Clinical Cancer Informatics. 2020;4:160-. https://doi.org/10.1200/CCI.19.00095

Vos, R. A., Katayama, T., Mishima, H., Paten, B. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research. 2020;9:136. https://doi.org/10.12688/f1000research.18236.1

Warren, W. C., Harris, R. A., Haukness, M., et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science(New York, N.Y.),370(6523). https://doi.org/10.1126/science.abc6617

Zoonomia Consortium. A comparative genomics multitool for scientific discovery and conservation. Nature. 2020;587(7833), 240–245. https://doi.org/10.1038/s41586-020-2876-6
2019

Armstrong J, et al. Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era. BioRxiv 730531. 2019. https://doi.org/10.1101/730531

Beyer W, Novak AM, Hickey G, Chan J, Tan V, Paten B, Zerbino D. Sequence tube maps: making graph genomes intuitive to commuters. Bioinformatics. 2019;35(24):5318-5320. https://doi.org/10.1093/bioinformatics/btz597

Ebler, J., Haukness, M., Pesout, T., Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biol. 2019;20:116. https://doi.org/10.1186/s13059-019-1709-0 

Frankish A, et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Research. 2019;47(D1):D766–D773. https://doi.org/10.1093/nar/gky955

HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;547(7777):187-192. https://doi.org/10.1038/s41586-019-1629-x 

Llamas B, et al. A strategy for building and using a human reference pangenome. Software Tool Article. 2019. https://doi.org/10.12688/f1000research.19630.1

Porubsky D, et al. A fully phased accurate assembly of an individual human genome. BioRxiv 855049. 2019. https://doi.org/10.1101/855049

Rosen YM, Paten BJ. An average-case sublinear forward algorithm for the haploid Li and Stephens model. Algorithms Mol Biol. 2019;14:11. https://doi.org/10.1186/s13015-019-0144-9

Sarsani V, et al. The genome of C57BL/6J “Eve”, the mother of the laboratory mouse genome reference strain. G3: Genes, Genomes, Genetics. 2019;9(6):1795-1805. https://doi.org/10.1534/g3.119.400071 

Sweeney NT, James KN, Nistorica A, Lorig-Roach RM, Feldheim DA. Expression of transcription factors divides retinal ganglion cells into distinct classes. J Comp Neurol. 2019;527(1):225-235. https://doi.org/10.1002/cne.24172

Torkzadehmahani R, Kairouz P, Paten B. Dp-cgan: Differentially private synthetic data and label generation. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops. 2019;0-0. 

Workman, R.E., et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat Methods. 2019;16:1297–1305. https://doi.org/10.1038/s41592-019-0617-2

2018

Armstrong J, Fiddes I, Diekhans M, Paten B. Whole-genome alignment and comparative annotation. Annual Review of Animal Biosciences. 2018;7:41-64. https://doi.org/10.1146/annurev-animal-020518-115005

Cline MS, et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLOS Genetics. 2018;14(12):e1007752. https://doi.org/10.1371/journal.pgen.1007752

Dang, L.T., et al. TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. BMC Genomics. 2018;19:238. https://doi.org/10.1186/s12864-018-4630-0

Fernandes J, et al. KRAB Zinc Finger Proteins coordinate across evolutionary time scales to battle retroelements. bioRxiv 429563. 2018. https://doi.org/10.1101/429563

Fiddes I, et al. Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation. Genome Res. 2018;28:1029-1038. https://doi.org/10.1101/gr.233460.117

Garrison, E., et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol. 2018;36:875–879. https://doi.org/10.1038/nbt.4227

Haussler D, Smuga-Otto M, Eizenga J, Paten B, Novak A, Nikitin S, Zueva M, Miagkov. A flow procedure for linearization of genome sequence graphs. Journal of Computational Biology. 2018;25(7). https://doi.org/10.1089/cmb.2017.0248

Heller P, Casaletto J, Ruiz G, Geller J. A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator. Sci Data. 2018;5:180156. https://doi.org/10.1038/sdata.2018.156

Jain, M., et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338–345. https://doi.org/10.1038/nbt.4060

Jain, M., Olsen, H., Turner, D., Stoddart, D., Bulazel, K., Paten, B., Haussler, D., Willard, H., Akeson, M., Miga, K. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol. 2018;36:321–323. https://doi.org/10.1038/nbt.4109

Kolmogorov M, et al. Chromosome assembly of large and complex genomes using multiple references. Genome Res. 2018;28:1720-1732. https://doi.org/10.1101/gr.236273.118

Kronenberg Z, et al. High-resolution comparative analysis of great ape genomes. Science. 2018;360(6393). https://doi.org/10.1126/science.aar6343

Lilue, J., et al. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet. 2018;50:1574–1583. https://doi.org/10.1038/s41588-018-0223-8

The Computational Pan-Genomics Consortium, Marschall T, Guryev V, Schonhuth A, Vandin F, Ye K. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics. 2018;19(1):118-135. https://doi.org/10.1093/bib/bbw089

Thybert D, et al. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res. 2018;28:448-459. https://doi.org/10.1101/gr.234096.117

Tunstall T, Kock R, Valhalla J, Diekhans M, Fiddes I, Armstrong J, Paten B, Ryder O, Steiner C. Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells. Genome Res. 2018;28:780-788. https://doi.org/10.1101/gr.227603.117

2017

Armstrong J, Hickey G, Diekhans M, Paten B. A comparative genomics multitool for scientific discovery and conservation. Manuscript number: 2017-06-07529. https://doi.org/10.1101/730531

GTEx Consortium, et al. Genetic effects on gene expression across human tissues. Nature. 2017;550: 204–213. https://doi.org/10.1038/nature24277

Haussler D, Smuga-Otto M, Eizenga J, Paten B. A flow procedure for linearization of genome sequence graphs. Journal of Computational Biology. 2018;25(7). https://doi.org/10.1089/cmb.2017.0248

Jagodnik K, et al. Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop. Journal of Biomedical Informatics. 2017;71:49-57. https://doi.org/10.1016/j.jbi.2017.05.006 

Li X, et al. The impact of rare variation on gene expression across tissues. Nature. 2017;550(7675):239-243. https://doi.org/10.1038/nature24267

Lincoln S, Yang S, Cline M, Kobayashi Y, Zhang C, Topper S, Haussler D, Paten B, Nussbaum R. Consistency of BRCA1 and BRCA2 Variant Classifications Among Clinical Diagnostic Laboratories. JCO Precision Oncology. 2017;1:1-10. https://doi.org/10.1200/PO.16.00020 

Novak, A.M., Garrison, E., Paten, B. A graph extension of the positional Burrows–Wheeler transform and its applications. Algorithms Mol Biol. 2017;12:18. https://doi.org/10.1186/s13015-017-0109-9 

O’Connor BD, Yuen D, Chung V, Duncan A, Liu X, Patricia J, Paten B, Stein L, Ferretti V. The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows. F1000Res. 2017;6:52. https://doi.org/10.12688/f1000research.10137.1

Paten B, Novak A, Eizenga J, Garrison E. Genome graphs and the evolution of genome inference. Genome Res. 2017;27:665-676. https://doi.org/10.1101/gr.214155.116 

Paten B., Novak A.M., Garrison E., Hickey G. (2017) Superbubbles, Ultrabubbles and Cacti. Research in Computational Molecular Biology. 2017;10229. https://doi.org/10.1007/978-3-319-56970-3_11 

Rand, A., Jain, M., Eizenga, J. Musselman-Brown A, Olsen H, Akeson M, Paten B. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14:411–413. https://doi.org/10.1038/nmeth.4189

Regev A, et al. The human cell atlas white paper. HCA Consortium. 2017. https://doi.org/10.48550/arXiv.1810.05192

Rice E, et al. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res. 2017;27:686-696. https://doi.org/10.1101/gr.213595.116

Rosen Y., Eizenga J., Paten B. Describing the Local Structure of Sequence Graphs. Algorithms for Computational Biology. 2017;10252. https://doi.org/10.1007/978-3-319-58163-7_2 

Rosen Y, Eizenga J, Paten B. Modelling haplotypes with respect to reference cohort variation graphs. Bioinformatics. 2017;33(14):i118–i123. https://doi.org/10.1093/bioinformatics/btx236 

Saha A, Kim Y, Gewirtz A, Jo B, Gao C, McDowell I, The GTEx Consortium, Engelhardt B, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res. 2017;27:1843-1858. https://doi.org/10.1101/gr.216721.116

Tan, M., et al. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550: 249–254. https://doi.org/10.1038/nature24041

Tukiainen T, et al. Landscape of X chromosome inactivation across human tissues Nature. 2017;550(7675):244-248. https://doi.org/10.1038/nature24265

Vivian, J., et al. Toil enables reproducible, open source, big biomedical data analyses. Nat Biotechnol.  35, 314–316 (2017). https://doi.org/10.1038/nbt.3772

Yang S, Cline M, Zhang C, Paten B, Lincoln S. Data sharing and reproducible clinical genetic testing: successes and challenges. Biocomputing. 2017;166-176. https://doi.org/10.1142/9789813207813_0017 

Yang F, Wang J, The GTEx Consortium, Pierce B, Chen L. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis. Genome Res. 2017;27:1859-1871. https://doi.org/10.1101/gr.216754.116

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182. https://doi.org/10.1126/science.1216830

2016
2015

Jain, M., Fiddes, I., Miga, K., Olsen, H., Paten, B., Akeson, M. Improved data analysis for the MinION nanopore sequencer.. Nature methods. 2015;12: 351–356. https://doi.org/10.1038/nmeth.3290

Koepfli K, Paten B, the Genome 10K Community of Scientists, O’Brien S. The Genome 10K Project: a way forward. Annual Review of Animal Biosciences. 2015;3:57-111. https://doi.org/10.1146/annurev-animal-090414-014900

Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, PatenB. Building a pan-genome reference for a population. J Comput Biol. 2015;22(5):387-401. https://doi.org/10.1089/cmb.2014.0146

Novak A, Rosen Y, Haussler D, Paten B. Canonical, stable, general mapping using context schemes. Bioinformatics. 2015; 31(22):3569–3576. https://doi.org/10.1093/bioinformatics/btv435

Paten B, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association. 2015;22(6):1143–1147. https://doi.org/10.1093/jamia/ocv047

Philippakis AA, et al. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat. 2015;36(10):915-921. https://doi.org/10.1002/humu.22858

Rosenbloom K, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Research. 2015;43(D1)D670–D681. https://doi.org/10.1093/nar/gku1177

Shafin MK, Kabir KL, Ridwan I, Anannya TT, Karim RS, Hoque MM, Rahman MS. Impact of heuristics in clustering large biological networks. Comput Biol Chem. 2015;59 Pt A:28-36. https://doi.org/10.1016/j.compbiolchem.2015.05.007

2014
2013
2012

Haussler D, et al. A million cancer genome warehouse. Defense Technical Information Center. 2012.

Westesson O, Lunter G, Paten B, Holmes I. Accurate reconstruction of insertion-deletion histories by statistical phylogenetics. PLoS One. 2012;7(4):e34572. https://doi.org/10.1371/journal.pone.0034572

Zerbino D, Paten B, Haussler D. Integrating genomes. Science. 2012;336(6078):179-182. https://doi.org/10.1126/science.1216830

2011

Earl D, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011;21(12):2224-2241. https://doi.org/10.1101/gr.126599.111

Paten B, Diekhans M, Earl D, St John J, Ma J, Suh B, Haussler D. Cactus graphs for genome comparisons. J Comput Biol. 2011;18(3):469-481. https://doi.org/10.1089/cmb.2010.0252

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011;21(9):1512-1528. https://doi.org/10.1101/gr.123356.111

Roskin, K.M., Paten, B. & Haussler, D. Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics. 2011;12:144. https://doi.org/10.1186/1471-2105-12-144

The ENCODE Project Consortium (2011). A User’s Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9(4): e1001046. https://doi.org/10.1371/journal.pbio.1001046

Westesson O, Lunter G, Paten B. Phylogenetic automata, pruning, and multiple alignment. 2011

2010
2009
2008

Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 2008;18(11):1814-1828. https://doi.org/10.1101/gr.076554.108

Paten B, Herrero J, Fitzgerald S, Beal K, Flicek, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 2008;18(11):1829-1843. https://doi.org/10.1101/gr.076521.108

2007
2005

Ettwiller L, Paten B, Souren M, Loosli F, Wittbrodt J, Birney E. The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol. 2005;6(12):R104. https://doi.org/10.1186/gb-2005-6-12-r104